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#' @title Convert phangorn reconstruction to a vector
#'
#' @description
#' Converts a character reconstruction from phangorn into a vector
#'
#' @param x The phyDat object that contains a character reconstruction from phangorn
#' @param site The character number to convert into a vector
#' @param best A logical indicating whether the state that maximizes some function (likelihood, parsimony, etc.) is to be returned.
#'
#' @details
#' Creates a vector that contains the best tips and node state from a phangorn reconstruction.
ConvertPhangornReconstructions <- function(x, site=1, best=TRUE) {
x.local <- subset(x, , site)
nc = attr(x.local, "nc")
y = matrix(unlist(x.local[]), ncol = nc, byrow = TRUE)
rownames(y) <- names(x.local[])
colnames(y) <- attr(x.local, "levels")
result <- y
if(best) {
best.vector <- rep(NA,nrow(result))
for (i in sequence(nrow(result))) {
best.vector[i] <- sample(which.max(result[i,]), 1) #so resolve ties randomly
}
names(best.vector) <-rownames(y)
result<-best.vector
}
return(result)
}
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